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Microsatellite loci are commonly used markers in population genetic studies. In this study, we present 40 novel and polymorphic microsatellite loci elaborated for the ichneumonid parasitoid Latibulus argiolus (Rossi, 1790). Reaction condition optimisation procedures allowed 14 of these loci to be co-amplified in two PCRs and loaded in two multiplex panels onto a genetic analyser. The assay was tested on 197 individuals of L. argiolus originating from ten natural populations obtained from the host nests of paper wasps. The validated loci were polymorphic with high allele numbers ranging from eight to 27 (average 17.6 alleles per locus). Both observed and expected heterozygosity values were high, ranging between 0.75 and 0.92 for HO (mean 0.83) and from 0.70 to 0.90 for HE (mean 0.85). The optimized assay showed low genotyping error rate and negligible null allele frequency. The designed multiplex panels could be successfully applied in relatedness analyses and genetic variability studies of L. argiolus populations, which would be particularly interesting considering the coevolutionary context of this species with its social host.

1986年に創刊された「データベース白書」は，2008年5月刊行の「電子情報サービス2008」をもって23年目となった。本稿では，この間の白書各年版の内容を振り返りつつ，わが国におけるデータベース関連諸分野の変動を跡づけ，今後の展望に資するものとしたい。

Although the hymenopteran sex-determining mechanism generally results in haploid males and diploid females, diploid males can be produced via homozygosity at the sex-determining locus. Diploid males have low fitness because they are effectively sterile or produce presumably sterile triploid offspring. Previously, triploid females were observed in three species of North American Polistes paper wasps, and this was interpreted as indirect evidence of diploid males. Here we report what is, to our knowledge, the first direct evidence: four of five early male-producing Polistes dominulus nests from three populations contained diploid males. Because haploid males were also found, however, the adaptive value of early males cannot be ignored. Using genetic and morphological data from triploid females, we also present evidence that both diploid males and triploid females remain undetected throughout the colony cycle. Consequently, diploid male production may result in a delayed fitness cost for two generations. This phenomenon is particularly relevant for introduced populations with few alleles at the sex-determining locus, but cannot be ignored in native populations without supporting genetic data. Future research using paper wasp populations to test theories of social evolution should explicitly consider the potential impacts of diploid males.

We reconstructed the broad backbone of conifer phylogeny from a survey of 15–17 plastid loci and associated noncoding regions from exemplar conifer species. Parsimony and likelihood analyses recover the same higher-order relationships, and we find strong support for most of the deep splits in conifer phylogeny, including those within our two most heavily sampled families, Araucariaceae and Cupressaceae. Our findings are broadly congruent with other recent studies, and are inferred with comparable or improved bootstrap support. The deepest phylogenetic split in conifers is inferred to be between Pinaceae and all other conifers (Cupressophyta). Our current gene and taxon sampling does not support a relationship between Pinaceae and Gnetales, observed in some published studies. Within the Cupressophyta clade, we infer well-supported relationships among Cephalotaxaceae, Cupressaceae, Sciadopityaceae, and Taxaceae. Our data support recent moves to recognize Cephalotaxus under Taxaceae, and we find strong support for a sister-group relationship between the two predominantly southern hemisphere conifer families, Araucariaceae and Podocarpaceae. A local hotspot of indel evolution shared by the latter two conifer families is identified in the coding portion of one of the plastid ribosomal protein genes. The removal of the most rapidly evolving plastid characters, as defined using a likelihood-based classification of substitution rates for the taxa considered here, is shown to have little to no effect on our inferences of higher-order conifer relationships.

Possible somatic DNA recombination in the brain has been investigated by attempting to capture direct or indirect evidence of it. Until recently, the biological significance of the DNA event, the genes is involved in the recombination, or even whether the event actually occurs in the brain has remained unclear. The DNA-rearranged locus-oriented approach and the recombination activity-oriented approach have mutually contributed to the elucidation of the biological features of extra-immune system somatic DNA recombination. There have been only 2 loci proposed for the candidate, one is a repetitive sequence and the other DNA recombination is nonrepetitive locus. This review states conventional concepts and discussions chronologically and finally to the newest aspects of DNA rearrangement in the brain.

The aim of this workshop was to present and to discuss recent findings and developments in the fields of regulation of gene function and expression, and of restriction enzyme analysis of DNA, with an effort to combine molecular aspects with certain new aspects of cytogenetics and developmental genetics of the mouse. A. G. Searle: Location of genes on the banded karyotype of the mouse M.R.C. Radiobiology Unit, Harwell, Oxon. OX11 ORD, U.K. J. Tonnes Nielsen: Distribution of amylase haplotypes in a feral Danish house mouse population Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus C, Denmark K. K. Thomsen, J. P. Hjorth and J. T. Nielsen: Variation in restriction pattern among mouse amylase gene-complexes Department of Molecular Biology and Plant Physiology, University of Aarhus, Denmark M. Meisler, T. K. Antonucci and M. Morley: Quantitative studies of the products of two pancreatic amylase genes in YBR mice Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, U.S.A. Roger S. Holmes: The alcohol dehydrogenase gene complex on chromosome 3 of the mouse School of Science, Griffith University, Nathan, 4111. Q. Australia S. A. M. Martin and Grahame Bulfield: Regulatory genes of mouse histidine decarboxylase Poultry Research Centre, Roslin EH25, 9PS, UK M. Frater-Schroder, O. Haller, R. Gmur, L. Kierat and S. Anastasi: Allelic forms of mouse transcobalamin 2 expressed in serum and by peritoneal macrophages Dept. of Pediatrics and Inst. for Immunology and Virology, University of Zurich, CH-8032 Zurich, Switzerland J. Peters and A. G. Searle: Influence of an X-autosome translocation on the Pgm-2 locus M.R.C. Radiobiology Unit, Harwell, Oxon. OX11 ORD, U.K. D. M. Hunt: Metallothionein and copper homeostasis in mottled mice School of Biological Sciences, Queen Mary College, University of London, London EL 4NS, England D. P. Lovell: Pharmacogenetics of barbiturate anaesthesia in mice MRC Laboratory Animals Centre, Woodmansterne Road, Carshalton, Surrey SM5 4EF, England J. Forejt: Mapping of a polymorphic gene locus for histocompatibility antigens of teratocarcinoma cells within the T-t complex of the mouse Institute of Molecular Genetics, Czechoslovak Academy of Sciences, 142 20 Praha 4, Czechoslovakia Lee M. Silver, Jane Uman, Jayne Danska and James Garrels: Molecular probes for the genomic organization and evolution of the mouse t complex Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Hans Lehrach, Dan Rohme, Annemarie Frischauf, Herbert Jackle and Jan-Erik Edstrom: Cloning of DNA fragments of the t region of chromosome 17 of the mouse European Molecular Biology Laboratory, Meyerhofstraβe 1, D-6900 Heidelberg, Germany G. Delarbre G. Gachelin H. Condamine P. Kourilsky: Use of an H-2 cDNA probe to map H-2tw32 genes Unite de Biologie Moleculaire du Gene, ER CNRS 201, SC INSERM 20, Unite de Genetique Cellulaire, Institut Pasteur, 25 rue du Dr. Roux, 75015 Paris, France Heinz Winking: Mode of action of t-mutants in sperm haplophase Institut fur Pathologie, Medizinische Hochschule Lubeck, D-2400 Lubeck, West Germany M. Boubelik, Z. Ŝpatenkova, J. Placy and J. Ĉapkova: Reaction of the normal mouse sera against antigens of the inbred chicken—interstrain differences Institute of Molecular Genetics, Czechoslovak Academy of Sciences, 142 20 Prague 4, ĈSSR K. Fischer Lindahl K. Burki: Maternal inheritance of a cell surface antigen in the mouse Basel Institute for Immunology, CH-4005 Basel, Switzerland and Laboratory of Cell Differentiation, University of Geneva, CH-1200 Geneva, Switzerland J. Hilkens, D. Schol, V. Kroezen, F. Buys, R. Nauta and J. Hilgers: Expression of endogenous MTV in somatic cell hybrids Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands N. G. Copeland, N. A. Jenkins and B. K. Lee: Association of the Lethal Yellow (AY) coat color mutation with an ecotropic MuLV provirus The Jackson Laboratory, Bar Harbor, Maine 04609, USA N. A. Jenkins and N. G. Copeland: Murine leukemia virus sequences associated with allels of the Dilute (d) coat color locus The Jackson Laboratory, Bar Harbor, Maine 04609, USA Susan Lindsay and Marilyn Monk: Methylation patterns on the active and inactive human X chromosome MRC Mammalian Development Unit, 4 Stephenson Way, London NW1 2HE, England C. L. Stewart, D. Jahner, H. Stuhlmann and R. Jaenisch: De novo methylation, expression and infectivity of retroviral genomes introduced into early mouse embryonic cells Heinrich-Pette-Institut, Martinistraβe 52, D-2000 Hamburg 20, West Germany L. Bolund, O. P. Clausen and P. K. A. Jensen: Chromatin organization in relation to cell differentiation Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark L.-G. Lundin: Paralogous genes and cell differentiation Department of Medical and Physiological Chemistry, Box 575, BMC, S-751 23 Uppsala, Sweden S. D. M. Brown: The organization and evolutionary progress of a dispersed repetitive family of sequences (MIF-1) in rodent genomes Equipe de Recherche de Biophysique, CNRS, USTL, 34060 Montpellier, France W. Traut H. Winking: Characterization of a new type of heterochromatin in the mouse Institut fur Biologic, Medizinische Hochschule, Lubeck, D-2400 Lubeck Institut fur Pathologie, Medizinische Hochschule Lubeck, D-2400 Lubeck, West Germany I. Somssich J. Spira H. Hameister G. Klein: Replication studies on mouse chromosomes Institut fur Humangenetik, Albertstraβe 11, D-7800 Freiburg, West Germany Department of Tumor Biology, Karolinska Institutet, S-104 01 Stockholm, Sweden R. Dofuku: A possible selective endomitotic origin of trisomy of chromosome 13: Karyological implications for murine mammary tumorigenesis Department of Cell Biology, Cancer Institute, Tokyo (Japanese Foundation for Cancer Research) V. C. Bode: Ethylnitosourea-induced mutations in the t-region of chromosome 17 Biology Division, Kansas State University, Manhattan, Kansas 66506, U.S.A. J. Peters: Some characterization of mutations induced by ENU in the mouse M.R.C. Radiobiology Unit, Harwell, Oxon OX11 ORD, U.K. F. Bonhomme J. L. Guenet J. Catalan: Sterility factors segregating in interspecific M. musculus L. x M. spretus Lataste crosses Laboratoire d'Evolution des Vertebres, Faculte des Sciences, 2, Place Eugene Bataillon, 34060 Montpellier CEDEX, France Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France B. M. Cattanach E. P. Evans M. Burtenshaw: X chromosomal location and variable inactivation of Sxr (Sex Reversed) in the mouse M.R.C. Radiobiology Unit, Harwell, Oxon OX11 ORD, U.K. Dunn School of Pathology, South Parks Road, Oxford, U.K. A. Gropp and H. Winking: Sex reversal in XY mice Institut fur Pathologie der Medizinischen Hochschule Lubeck, D-2400 Lubeck, West Germany K. Moriwaki H. Yonekawa T. Shiroishi N. Miyashita T. Sagai H. T. Imai: Genetic profile of Mus musculus various subspecies from view points of cyto-, biochemical- and immunogenetics Department of Cytogenetics, National Institute of Genetics, Mishima, Shizuoka-ken 411, Japan Department of Biochemistry, Saitama Cancer Center Research Institute, Ina-machi, Saitama-ken, 362, Japan

The capsular polysaccharide (CPS) synthesis locus of Streptococcus pneumoniae serotype 9V was amplified by long-range PCR and sequenced. The locus was 17368 bp in size and contained 15 ORFs. The genetic organization of the cluster shared many features with other S. pneumoniae capsule loci, including the presence of four putative regulatory genes at the 5′ end. Comparative sequence analyses allowed putative functions to be assigned to each of the gene products. The ORFs appeared to encode, besides the four regulatory genes, five glycosyltransferases, two O-acetyltransferases, an N-acetylglucosamine 2-epimerase, a glucose 6-dehydrogenase, an oligosaccharide transporter protein and a polysaccharide repeating unit polymerase. These functions covered the steps proposed in the CPS biosynthesis of serotype 9V. TLC of carbohydrate intermediates formed after incubation of bacterial membrane preparations with 14C-labelled precursors demonstrated that the fifth ORF (cps9vE) encoded a UDP-glucosyl-1-phosphate transferase. This function was confirmed with the help of a cps9vE mutant that carried a deletion of a guanine residue located adjacent to a stretch of adenines. The identification and characterization of the serotype 9V locus is a major step in unravelling the 9V capsule biosynthesis pathway and broadens the insight into the genetic diversity of the S. pneumoniae capsule loci.

Lipooligosaccharide (LOS) is a major virulence factor of the pathogenic Neisseria. Nine lgt genes at three chromosomal loci (lgt-1, 2, 3) encoding the glycosyltransferases responsible for the biosynthesis of LOS oligosaccharide chains were examined in 26 Neisseria meningitidis, 51 Neisseria gonorrhoeae and 18 commensal Neisseria strains. DNA hybridization, PCR and nucleotide sequence data were compared to previously reported lgt genes. Analysis of the genetic organization of the lgt loci revealed that in N. meningitidis, the lgt-1 and lgt-3 loci were hypervariable genomic regions, whereas the lgt-2 locus was conserved. In N. gonorrhoeae, no variability in the composition or organization of the three lgt loci was observed. lgt genes were detected only in some commensal Neisseria species. The genetic organization of the lgt-1 locus was classified into eight types and the lgt-3 locus was classified into four types. Two types of arrangement at lgt-1 (II and IV) and one type of arrangement at lgt-3 (IV) were novel genetic organizations reported in this study. Based on the three lgt loci, 10 LOS genotypes of N. meningitidis were distinguished. Phylogenetic analysis revealed a gene cluster, lgtH, which separated from the homologous genes lgtB and lgtE. The lgtH and lgtE genes were mutually exclusive and were located at the same position in lgt-1. The data demonstrated that pathogenic and commensal Neisseria share a common lgt gene pool and horizontal gene transfer appears to contribute to the genetic diversity of the lgt loci in Neisseria.

A key intermediate for biodegradation of various distinct aromatic growth substrates in Comamonas testosteroni is protocatechuate (Pca), which is metabolized by the 4,5-extradiol (meta) ring fission pathway. A locus harbouring genes from C. testosteroni BR6020 was cloned, dubbed pmd, which encodes the enzymes that degrade Pca. The identity of pmdAB, encoding respectively the α- and β-subunit of the Pca ring-cleavage enzyme, was confirmed by N-terminal sequencing and molecular mass determination of both subunits from the separated enzyme. Disruption of pmdA resulted in a strain unable to grow on Pca and a variety of aromatic substrates funnelled through this compound (m- and p-hydroxybenzoate, p-sulfobenzoate, phthalate, isophthalate, terephthalate, vanillate, isovanillate and veratrate). Growth on benzoate and o-aminobenzoate (anthranilate) was not affected in this strain, indicating that these substrates are metabolized via a different lower pathway. Tentative functions for the products of other pmd genes were assigned based on sequence identity and/or similarity to proteins from other proteobacteria involved in uptake or metabolism of aromatic compounds. This study provides evidence for a single lower pathway in C. testosteroni for metabolism of Pca, which is generated by different upper pathways acting on a variety of aromatic substrates.

Antigenic variation of gonococcal pilin involves a family of variable genes that undergo homologous recombination, resulting in transfer of variant sequences from the pilS silent gene copies into the complete pilE expression locus. Little is known about the specific recombination events that are involved in assembling new variant pilin genes in vivo. One approach to understanding pilin variation in vivo is to carry out experimental human infections with a gonococcal strain having a fully characterized repertoire of pilin genes, so that the specific recombination events occurring in vivo can be determined. To this end, the authors cloned, sequenced and mapped the pilin genes of strain FA1090 of Neisseria gonorrhoeae. This strain contains one pilE locus and 19 silent gene copies that are arranged in five pilS loci; the pilE locus and four of the pilS loci are clustered in a 35 kb region of the chromosome. The general features of the pilin loci in FA1090 are similar to those in strain MS11, in which the mechanism of pilin variation has been extensively studied. However, none of the silent copy sequences are identical in the two strains, which emphasizes the extreme variability in this gene family among gonococci. Three male volunteers were inoculated with the same variant of strain FA1090 and developed urethritis within 2–4 d. The pilE gene sequences from a total of 23 colonies cultured from the subjects were analysed, determining which pilS silent copy donated each portion of the expressed pilE genes. There were 12 different pilin variants, one of which was the original inoculum variant, among the in vivo-expressed pilE gene sequences. The pilE of the inoculum variant was derived entirely from a single silent copy (pilS6c1). However, the pilE genes in the majority of the colonies cultured from the infected subjects were chimeras of sequence derived from two or three silent copies. Recombination to generate new pilE sequences involved exchange of single variable minicassettes, multiple minicassettes, entire silent gene copies, or (rarely) recombination within a minicassette.

The sequence of a cloned genomic fragment of Trichomonas vaginalis containing a complete actin gene was determined. An uninterrupted open reading frame of 1128 nucleotides was found that codes for an actin gene. Two overlapped consensus promoter sequences for T. vaginalis were found 12 nucleotides upstream the actin initiation codon. In addition to actin, two incomplete open reading frames were found at the 5′ and 3′ ends of the clone. These two sequences are expressed and showed similarity to adenylate cyclase genes and a yeast hypothetical protein. The overall sequence showed a higher G+C content and a lower frequency of repeated sequences in the coding regions when compared with the non-coding regions. A similar unequal nucleotide distribution was found in various T. vaginalis genes retrieved from data bases.

Mycobacterium avium subsp. paratuberculosis is a pathogen that causes chronic inflammation of the intestine in many animals, including primates, and is implicated in Crohn’s disease in humans. It differs from other members of the M. avium complex in having 14–18 copies of IS900 inserted into conserved loci in its genome. In the present study, genomic DNA flanking 14 of these insertions was characterized and homologues in the Mycobacterium tuberculosis and M. avium subsp. avium genomes were identified. These included regions encoding a sigma factor (sigJ) at locus 3, a nitrate reductase (nirA) at locus 4, a transcription regulator (tetR) and polyketide synthase at locus 6, and a 6-O-methylguanine methyltransferase at locus 9. In addition, locus numbers were assigned to 9 of 15 RFLP bands previously described. IS900 insertion at 7 of the 14 characterized loci was into the RBS of a gene substituting an RBS encoded by IS900 sited two bases closer to the initiation codon. IS900 insertion at five loci interrupted an ORF at the target site, one of which encoded a homologue of the immunodominant mycobacterial DesA1 protein. Eleven of eighty-one M. avium subsp. paratuberculosis isolates lacked the insertion site at locus 6 together with flanking genomic DNA. This region was also absent from seven reference strains of M. avium subsp. avium, from one M. avium subsp. silvaticum and from six other mycobacterial species. A multiplex PCR of IS900 loci (MPIL) typing method was developed which was able to discriminate 10 different types of M. avium subsp. paratuberculosis from the panel of 81 isolates with consistent differences between those of bovine and ovine origin. Nine MPIL types corresponded with a single PstI/BstEII RFLP type, suggesting that this method may be applicable to typing of M. avium subsp. paratuberculosis directly from a sample without the need for culture. The remaining MPIL type corresponded with seven PstI/BstEII RFLP types. Further resolution of these may come from sequencing the remaining four uncharacterized IS900 loci.

The opportunistic fungal pathogen Candida albicans is asexual and diploid. Thus, introduction of recessive mutations requires targeted gene replacement of two alleles to effect expression of a recessive phenotype. This is often performed by recycling of a URA3 marker gene that is flanked by direct repeats of hisG. After targeting to a locus, recombination between the repeats excises URA3 leaving a single copy of hisG in the disrupted allele. The remaining functional allele is targeted in a second transformation with the same URA3 marked construct. Replacement can be highly biased toward one allele. At the PHR1 locus, there was an approximately 50-fold preference for replacement of the disrupted versus the functional allele in a heterozygous mutant. This preference was reduced six- to eightfold when the transforming DNA lacked the hisG repeats. Nonetheless, there remained a sixfold preference for targeting a particular allele of PHR1 and this was evident even in transformations of the parental strain containing two wild-type alleles of PHR1. Both wild-type alleles were cloned and nucleotide sequence comparison revealed 24 heterologies over a 2 kb region. Using restriction site polymorphisms to distinguish alleles, it was observed that transformation with the cloned DNA of allele PHR1-1 preferentially targeted allele 1 of the genome. Transformations with PHR1-2 exhibited the reciprocal specificity. In both these instances, heterology was present in the flanking regions of the transforming DNA. When the transforming DNA was chosen from a region 100% identical in both alleles, alleles 1 and 2 were targeted with equal frequency. It is concluded that sequence heterology between alleles results in an inherent allele specificity in targeted recombination events.

The pattern of expression of the genes involved in the utilization of aryl beta-glucosides such as arbutin and salicin is different in the genus Shigella compared to Escherichia coli. The results presented here indicate that the homologue of the cryptic bgl operon of E. coli is conserved in Shigella sonnei and is the primary system involved in beta-glucoside utilization in the organism. The organization of the bgl genes in 5. sonnei is similar to that of E. coli; however there are three major differences in terms of their pattern of expression. (i) The bglB gene, encoding phospho-beta-glucosidase B, is insertionally inactivated in 5. sonnei. As a result, mutational activation of the silent bgl promoter confers an Arbutin-positive (Arb(+)) phenotype to the cells in a single step; however, acquiring a Salicin-positive (Sal(+)) phenotype requires the reversion or suppression of the bglB mutation in addition. (ii) Unlike in E. coli, a majority of the activating mutations (conferring the Arb(+) phenotype) map within the unlinked hns locus, whereas activation of the E. coli bgl operon under the same conditions is predominantly due to insertions within the bglR locus. (iii) Although the bgl promoter is silent in the wild-type strain of 5. sonnei (as in the case of E. coli), transcriptional and functional analyses indicated a higher basal level of transcription of the downstream genes. This was correlated with a 1 bp deletion within the putative Rho-independent terminator present in the leader sequence preceding the homologue of the bglG gene. The possible evolutionary implications of these differences for the maintenance of the genes in the cryptic state are discussed.

This paper reports the first direct molecular evidence that X chromosome loss during determination of male aphids (XO) is random. Clonal and sexual females, and males, of the species Sitobion near fragariae were screened using three polymorphic microsatellite loci. Two loci, Sm10 and Sm17, showed the same heterozygous genotypes in all three aphid morphs. The third, Sm11, was heterozygous for the same two alleles in clonal and sexual females, but of the 25 males screened 11 showed the ‘160’ allele and 14 showed the ‘156’ allele. This result indicates X-linkage of locus Sm11, with random loss of the X chromosome during the formation of male embryos. The possible implications of this result are discussed with respect to aphid sex determination, recombination and chromosome evolution.

The cyclic tetrapeptide HC-toxin is required for pathogenicity of the filamentous fungus Cochliobolus carbonum on maize. HC- toxin production is controlled by a complex locus, TOX2. The isolation and characterization of a new gene of the TOX2 locus, TOXF, is reported. It is shown that TOXF is specifically required for HC-toxin production and pathogenicity. It is present as two or three copies in all HC-toxin-producing (Tox2+ ) isolates and is absent in toxin-non-producing strains. The deduced amino acid sequence of TOXF has moderate homology to many known or putative branched-chain-amino-acid transaminases from various species. A strain of C. carbonum with all copies of TOXF disrupted grew normally but lost HC-toxin production and pathogenicity. It is proposed that TOXF has a biosynthetic role in HC-toxin synthesis, perhaps to aminate a precursor of Aeo (2- amino-9,10-epoxi-8-oxodecanoic acid).

Neisseria meningitidis strains express a diverse range of lipopolysaccharide (LPS) structures that have been classified into 12 immunotypes. A feature of meningococcal LPS is the reversible, high-frequency switching of expression (phase variation) of terminal LPS structures. A number of studies are strongly suggestive of a key role for these terminal structures, and their phase-variable expression, in pathogenesis. In a previous study, a locus of three LPS biosynthetic genes, lgtABE, involved in the biosynthesis of one of these terminal structures, lacto-N-neotetraose, was described. The molecular mechanism of phase-variable expression of this structure is by high-frequency mutation in a homopolymeric tract of G residues in the lgtA gene. To investigate the genetic basis of the structural differences between the immunotypes, and the potential for strains to express alternative immunotypes, this locus was examined in all of the immunotype strains. Initially, the lgt locus of strain 126E, an L1 immunotype strain, was cloned and sequenced, revealing two active genes, lgtC and lgtE. The remnants of the lgtA and lgtB genes and an inactive lgtD gene were also present, indicating that the locus may have once contained five active genes, similar to a locus previously reported in Neisseria gonorrhoeae strain F62. Probes based on each of the lgt genes (ABCDE), and the recently reported lgtG gene, were used to determine the presence or absence of lgt genes within individual strains, allowing the prediction of the phase variation repertoire of these strains. Sequencing to determine the nature of homopolymeric tract regions within the lgt genes was carried out to establish the potential for LPS switching. In general, the set of strains examined could be sorted into two distinct groups: one group which phase-vary the α-chain extension via lgtA or lgtC but cannot make β-chain; the second group phase-vary the β-chain extension via lgtG but do not vary α-chain (lacto-N-neotetraose).

The complexity of multigene families encoding rhoptry proteins and the generation of new variants in these families are constraints to development of vaccines incorporating rhoptry proteins. For example, the Babesia bigemina rhoptry associated protein (rap)-1 locus is composed of tandemly arranged genes including four polymorphic rap-1a genes and two classes of divergent genes, rap-1b and rap-1c. B. bigemina rap-1 polymorphism reflects recombination and gene conversion and results in multiple RAP-1 proteins with unique B- and T-cell epitopes. Is this complex locus structure and recombination a required feature of the rap-1 gene family among Babesia species? We addressed this question by analysis of the rap-1 locus in B. bovis. Sequence analysis of an 11 kb genomic clone representing the B. burn rap-1 locus revealed only two identical and continuous rap-1a gene copies, rap 1a-1 and rap-1a-2, located in a similar head to tail orientation. Using the conserved ig gene as a marker for the 3' boundary of the rap-1 locus, we conclude that divergent rap-1b and rap-1c genes, present in B. bigemina, are not similarly cis-linked to the B. bovis rap-1 locus. Analysis of the rap-1a genes 1 and 2 from each of multiple B. bovis strains from North and South America demonstrated RAP-1 size conservation with very limited amino acid sequence variation. The results suggest that the simple two gene arrangement in the B. bovis rap-1 gene family was generated by gene duplication and, in contrast to the B. bigemina rap-1 locus, both genes evolved together using homogenization mechanisms with point mutation as the single mechanism for gene variation. Three discontinuous non-rap-1 genes are closely cis-linked to the B. bovis rap-1 locus and the presence of multiple introns in these genes may limit rap-1 gene variation due to unequal crossing over. The different mechanisms likely involved in the evolution of the rap-1 family in B. bigemina versus B. bovis are reflected in the marked structural and antigenic polymorphism in the B. bigemina RAP-1 molecules as compared with the essentially monomorphic RAP-1 in B. bovis.

The rhoptry-associated protein-1 (RAP-1) of Babesia bigemina induces protective immune responses in cattle. RAP-1 has two regions of sequence dimorphism at the carboxy and amino terminal ends, respectively. Neutralization-sensitive, surface-exposed B-cell epitopes are present in the amino terminal variant type 1 (NT-1), and CD4+ T-cell epitopes in the carboxy terminal variant type 1 (CT-1). Importantly, antibodies recognizing NT-1 epitopes do not cross react with NT-2 and CD4+ T-cells recognizing epitopes in CT-1 do not cross react with CT-2, suggesting that variation in dimorphic regions of RAP-1 is immunologically significant. We evaluated rap-1 locus structure and the extent of sequence variation in the dimorphic regions of rap-1 genes from geographically diverse strains of B. bigemina. All strains contained NT-1 and NT-2 the encoding sequences were highly conserved, with at least 99% nucleotide identity among strains. However, the Puerto Rico strain encoded a hybrid NT-1/NT-2 sequence which appears to have originated by a gene conversion event. The 3′ ends of rap-1 genes, which include the carboxy terminal variants, are conserved among strains. A new and conserved CT variant (CT-3), with a region of sequence identity to CT-2 and a sequence not related to either CT-1 or CT-2, was identified in all strains of B. bigemina. All but one strain encode both NTs and the three CT variants. The S1A strain, an attenuated strain from Argentina, does not encode CT-2. While NT-1 is associated only with CT-1, NT-2 can be associated with all three CT variants in RAP-1. Within the genome, rap-1 genes are arranged in tandem repeats but with different gene copy number and arrangements among strains. Collectively, the data suggest that gene conversion and unequal recombination events contribute to overall rap-1 sequence conservation among gene variants and strains but may also generate new rap-1 variants.

The expressed sequence tag (EST) dataset of Toxoplasma gondii provides a wealth of information towards gene discovery. The complete cDNA and genomic sequence of EST tgc050 locus shows that it contains five copies of the conserved thrombospondin (TSP)-like motif present in a number of molecules with adhesive properties. A conserved region implicated with the adhesive characteristic of another group of proteins including several integrins, is also present in this molecule. The protein encoded by this sequence (rc50) is strongly recognised by monoclonal antibodies to MIC2. Affinity purified anti-rc50 antisera specifically reacted with a single protein of identical molecular mass as MIC2 and exclusively labeled the micronemes of T. gondii by cryo-immunoelectron microscopy. These results demonstrate that c50 encodes for MIC2, a previously characterised microneme protein of T. gondii. The extensive sequence similarity across multiple protein domains provides evidence that the protein encoded by this locus is the homologue to the Etp100 microneme protein of Eimeria tenella.

Review of the molecular characteristics of the variants identified at a series of disease loci suggests significant differences among loci in the relative frequency of nucleotide substitutions versus more complex events such as deletions. Some common features are repeatedly observed in each class of variant. For example, a high proportion of the nucleotide substitutions involve transitions of deoxycytidine and are suggested to result from deamination of cytosine at 5-methyl-CpG sites. Similarly, deletions of three or fewer nucleotides are relatively common in the non-nucleotide substitution class and these deletions are often associated with a seven-nucleotide core sequence. A significant fraction of the larger deletions and rearrangements may be associated with repetitive elements. Many of the deletion events do not appear to involve a chromosomal recombination mechanism. Mechanisms involving transcription slippage and chromatid exchange have been suggested as possible alternative mechanisms for generating deletion events. The spectrum of mutational events identified, e.g. nucleotide substitutions versus deletions, differs between loci and is probably a reflection of both the gene structure and the selective pressure to generate a disease phenotype. This locus specificity (at both the biological and molecular level) would appear to have significant potential to compromise estimates of increases in the gene germinal mutation rate following exposure to mutagenic agents.

42 compounds identified in pulp mill effluent were screened for genetic activity in growing yeast cells using strains D7 and XV185-14C without S9. In addition to 3 of these compounds that had been shown previously to be mutagenic in Salmonella, 5 more were mutagenic in strain XV185-14C. All 8 induced 2–5-fold increases in reversion frequencies over background at the trp5 locus — 5 of these induced 1.5-3-fold increases at the hom3 locus and 1 induced a doubling at his1. None of the compounds induced absolute increases of gene convertants per plate in strain D7, although 3 showed increased convertant frequencies as survival decreased.

THE POTENTIAL APPLICATIONS of gene therapy are many, extending from monogenic hereditary diseases to acquired and multifactorial disorders. Therapeutic gene transfer addressing such a variety of conditions is currently being investigated, creating therapeutic options for diseases where none had previously been available. The field of gene therapy represents one of the most challenging therapeutics for the new millennium. As such the concept might have been oversold ahead of its time. Nevertheless, in some instances, potential clinical efficacy is currently being found with reports of significant successes, for example, in inherited severe combined immunodeficiency disorders (SCID), hemophilia, arteritis obliterans, and even cancer (CavazzanaCalvo et al., 2000; Cohen, 2000; Heise et al., 2000; Kay et al., 2000). The development of recombinant DNA technology has caused fear in the public and speculation regarding its potential risks. Public reaction to the implementation of gene therapy is at best ambivalent, ranging from enthusiasm about its formidable therapeutic promises to apprehension concerning its putative harmful consequences. Indeed, the report of accidents in the United States resulted in a broad debate on the subject of gene therapy regulation brought to the attention of the U.S. Senate and Government (Barinaga, 2000; Commander, 2000; Hollon, 2000a,b; Marshall, 2000; Renault, 2000). In addition, the recent occurrence of a malignant proliferation of the hematopoietic system in one gene therapy-treated SCID patient has been reported (www.astg.org). (Check and Schiermeier, 2002) with a monoclonal insertion of the retrovirus vector at a sensitive locus (LMO2).

XANTHINE dehydrogenase from Drosophila melanogaster is of particular interest since mutants at two separate loci lack this enzyme1 while a mutant at a third locus produces about 25 per cent of normal activity2. In an effort to detect strains of flies with genetically altered forms of xanthine dehydrogenase we devised a technique involving paper-strip electrophoresis in which this enzyme is located after electrophoresis by spraying the strip with the enzyme's substrates, incubating it at 25° C, and then using paper chromatography to separate the fluorescent product from the substrate which also fluoresces. This technique is very simple, and has potential application to other enzymes. Paper electrophoresis of xanthine dehydrogenase in rat serum has previously been reported using the technique of elution and direct assay3,4.

Summary Tabby patterns of fur coats are defining characteristics in wild and domestic felids. Historically, three autosomal alleles at one locus (Tabby): Abyssinian (Ta; a.k.a. ticked), mackerel (Tm; a.k.a. striped) and blotched (tb; a.k.a. classic, blotched) were thought to control these patterns in domestic cats and their breeds. Currently, at least three loci influence cat tabby markings, two of which are designated Tabby and Ticked. The Tabby locus is laeverin (LVRN) and affects the mackerel and blotched patterns. The unidentified gene for the Ticked locus on cat chromosome B1 was suggested to control the presence or absence of the ticked pattern (Tabby – Abyssinian (Ta; a.k.a. ticked). The cat reference genome (Cinnamon, the Abyssinian) has the ticked phenotype and the variant dataset and coat phenotypes from the 99 Lives Cat Genome Consortium (195 cats) were used to identify candidate genes and variants associated with the Ticked locus. Two strategies were used to find the Ticked allele(s), one considered Cinnamon with the reference allele or heterozygous (Strategy A) and the other considered Cinnamon as having the variant allele or heterozygous (Strategy B). For Strategy A, two variants in Dickkopf Wnt Signaling Pathway Inhibitor 4 (DKK4), a p.Cys63Tyr (B1:41621481, c.188G>A) and a less common p.Ala18Val (B1:42620835, c.53C>T) variant are suggested as two alleles influencing the Ticked phenotype. Bioinformatic and molecular modeling analysis suggests that these changes disrupt a key disulfide bond in the Dkk4 cysteine‐rich domain 1 or Dkk4 signal peptide cleavage respectively. All coding variants were excluded as Ticked alleles using Strategy B.

White coat patterning is a feature of many dog breeds and is known to be coded primarily by the gene micropthalmia-associated transcription factor (MITF). This patterning in the coat can be modified by other factors to produce the attractive phenotypes termed ‘ticked’ and ‘roan’ that describe the presence of flecks of color that vary in distribution and intensity within otherwise ‘clear’ white markings. The appearance of the pigment in the white patterning caused by ticking and roaning intensifies in the weeks after birth. We applied genome-wide association to compare English Cocker Spaniels of roan phenotype (N = 34) with parti-color (non-roan) English Cocker Spaniels (N = 9) and identified an associated locus on CFA 38, CFA38:11 057 040 (Praw = 8.9 × 10−10, Pgenome = 2.7 × 10−5). A local case–control association in English Springer Spaniels comparing 11 ticked and six clear dogs identified indicative association with a different haplotype, CFA38:11 122 467G>T (Praw = 1.7 × 10−5) and CFA38:11 124 294A>C (Praw = 1.7 × 10−5). We characterize three haplotypes in Spaniels according to their putative functional variant profiles at CFA38:11 111 286C>T (missense), CFA38:11 131 841–11 143 239DUP.insTTAA (using strongly linked marker CFA38:11 143 243C>T) and CFA38:11 156 425T>C (splice site). In Spaniels, the haplotypes work as an allelic series including alleles (t, recessive clear; T, dominant ticked/parti-color; and TR, incomplete dominant roan) to control the appearance of pigmented spots or flecks in otherwise white areas of the canine coat. In Spaniels the associated haplotypes are t (CCT), T (TCC) and TR (TTT) for SNP markers on CFA38 at 11 111 286C>T, 11 143 243C>T and 11 156 425T>C respectively. It is likely that other alleles exist in this series and together the haplotypes result in a complex range of patterning that is only visible when dogs have white patterning resulting from the epistatic gene Micropthalmia-associated transcription factor (the S-locus).

Freezing tolerance of triticale is a major trait contributing to its winter hardiness. The identification of genomic regions – quantitative trait loci (QTLs) and molecular markers associated with freezing tolerance in winter hexaploid triticale was the aim of this study. For that purpose a new genetic linkage map was developed for the population of 92 doubled haploid lines derived from ‘Hewo’ × ‘Magnat’ F1 hybrid. Those lines, together with parents were subjected to freezing tolerance test three times during two winter seasons. Plants were grown and cold-hardened under natural fall/winter conditions and then subjected to freezing in controlled conditions. Freezing tolerance was assessed as the plants recovery (REC), the electrolyte leakage (EL) and chlorophyll fluorescence parameters (JIP) after freezing. Three consistent QTLs for several fluorescence parameters, electrolyte leakage and the percentage of the survived plants were identified with composite interval mapping (CIM) and single marker analysis (SMA). The first locus Qfr.hm-7A.1 explained 9 % of variation of both electrolyte leakage and plants recovery after freezing. Two QTLs explaining up to 12 % of variation in plants recovery and shared by selected chlorophyll fluorescence parameters were found on 4R and 5R chromosomes. Finally, main locus Qchl.hm-5A.1 was detected for chlorophyll fluorescence parameters that explained up to 19.6 % of phenotypic variation. The common QTLs located on chromosomes 7A.1, 4R and 5R, clearly indicated physiological and genetic relationship of the plant survival after freezing with the ability to maintain optimal photochemical activity of the photosystem II and preservation of the cell membranes integrity. The genes located in silico in the identified QTLs include those encoding transmembrane helix proteins like potassium channel and phosphoric ester hydrolase involved in response to osmotic stress as well as proteins involved in the regulation of the gene expression, chloroplast RNA processing and pyrimidine salvage pathway. Additionally, our results confirm that the JIP test is a valuable tool to evaluate freezing tolerance of triticale under unstable winter environments.

Summary A higher minimum (night‐time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored.We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome‐wide association analysis identified several HNT‐specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions.A novel locus contributing to grain width under HNT conditions colocalized with Fie1, a component of the FIS‐PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript‐level response of Fie1 in grains developing under HNT stress.We present evidence to support the role of Fie1 in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.

Summary NPR1 has been found to be a key transcriptional regulator in some plant defence responses. There are nine NPR1 homologues (TaNPR1) in wheat, but little research has been done to understand the function of those NPR1‐like genes in the wheat defence response against stem rust (Puccinia graminis f. sp. tritici) pathogens.We used bioinformatics and reverse genetics approaches to study the expression and function of each TaNPR1.We found six members of TaNPR1 located on homoeologous group 3 chromosomes (designated as TaG3NPR1) and three on homoeologous group 7 chromosomes (designated as TaG7NPR1). The group 3 NPR1 proteins regulate transcription of SA‐responsive PR genes. Downregulation of all the TaNPR1 homologues via virus‐induced gene co‐silencing resulted in enhanced resistance to stem rust. More specifically downregulating TaG7NPR1 homeologues or Ta7ANPR1 expression resulted in stem rust resistance phenotype. By contrast, knocking down TaG3NPR1 alone did not show visible phenotypic changes in response to the rust pathogen. Knocking out Ta7ANPR1 enhanced resistance to stem rust. The Ta7ANPR1 locus is alternatively spliced under pathogen inoculated conditions.We discovered a new mode of NPR1 action in wheat at the Ta7ANPR1 locus through an NB‐ARC–NPR1 fusion protein negatively regulating the defence to stem rust infection.

Summary MicroRNAs (miRNAs) are a class of small noncoding RNAs that play important roles in plant growth and development as well as in stress responses. However, little is known about their regulatory functions affecting rice grain yield.We functionally characterized a novel miRNA in rice, OsmiR530, its target OsPL3, and its upstream regulator phytochrome‐interacting factor‐like 15 (OsPIL15). Their effects on rice yield were dissected comprehensively.We determined that OsmiR530 negatively regulates grain yield. Blocking OsmiR530 increases grain yield, whereas OsmiR530 overexpression significantly decreases grain size and panicle branching, leading to yield loss. Additionally, OsPL3, which encodes a PLUS3 domain‐containing protein, is targeted directly by OsmiR530. Knocking out OsPL3 decreases the grain yield. In‐depth analyses indicated that OsPIL15 activates OsMIR530 expression by directly binding to the G‐box elements in the promoter. Analyses of genetic variations suggested that the OsMIR530 locus has likely been subjected to artificial selection during rice breeding.The results presented herein reveal a novel OsPIL15–OsmiR530 module controlling rice grain yield, thus providing researchers with a new target for the breeding of high‐yielding rice.

Motivation Quantification of isoform abundance has been extensively studied at the mature RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA sequencing. Results We address this problem with a new computational method called Deconvolution of Expression for Nascent RNA-sequencing data (DENR), which models nascent RNA-sequencing read-counts as a mixture of user-provided isoforms. The baseline algorithm is enhanced by machine-learning predictions of active transcription start sites and an adjustment for the typical ‘shape profile’ of read-counts along a transcription unit. We show that DENR outperforms simple read-count-based methods for estimating gene and isoform abundances, and that transcription of multiple pre-RNA isoforms per gene is widespread, with frequent differences between cell types. In addition, we provide evidence that a majority of human isoform diversity derives from primary transcription rather than from post-transcriptional processes. Availability and implementation DENR and nascentRNASim are freely available at https://github.com/CshlSiepelLab/DENR (version v1.0.0) and https://github.com/CshlSiepelLab/nascentRNASim (version v0.3.0). Supplementary information Supplementary data are available at Bioinformatics online.

To examine the role of S100B in genetic susceptibility to Alzheimer's disease (AD), we conducted a case-control study to analyze four polymorphism loci (rs2839364, rs1051169, rs2300403, and rs9722) of the S100B gene and AD risk. We found an independent increased risk of AD in ApoE e4(-) subjects carrying the rs9722 AA-genotype (OR = 2.622, 95% CI = 1.399-4.915, P = 0.003). Further investigation revealed the serum S100B levels to be lower in rs9722 GG carriers than in rs9722 AA carriers (P = 0.003). We identified three miRNAs (miR-340-3p, miR-593-3p, miR-6827-3p) in which the seed match region covered locus rs9722. Luciferase assays indicated that the rs9722 G allele has a higher binding affinity to miR-6827-3p than the rs9722 A allele, leading to a significantly decreased fluorescence intensity. Subsequent western blot analysis showed that the S100B protein level of SH-SY5Y cells, which carry the rs9722 G allele, decreased significantly following miR-6827-3p stimulation (P = 0.009). The present study suggests that the rs9722 polymorphism may upregulate the expression of S100B by altering the miRNA binding capacity and may thus increase the AD risk. This finding would be of great help for the early diagnosis of AD.

Inherited predispositions to acute lymphoblastic leukemia have been well investigated in pediatric patients, but studies on adults, particularly Chinese patients, are limited. In this study, we conducted a genome-wide association study in 466 all-age Chinese patients with Acute lymphoblastic leukemia (ALL) and 1,466 non-ALL controls to estimate the impact of age on ALL susceptibility in the Chinese population. Among the 17 reported loci, 8 have been validated in pediatric and 1 in adult patients. The strongest association signal was identified at ARID5B locus and gradually decreased with age, while the signal at GATA3 exhibited the opposite trend and significantly impact on adult patients. With genome-wide approaches, germline variants at 2q14.3 rank as the top inherited predisposition to adult patients (e.g., rs73956024, P = 4.3 × 10-5) and separate the genetic risk of pediatric vs. adult patients (P = 3.6 × 10-6), whereas variants at 15q25.3 (e.g., rs11638062) have a similar impact on patients in different age groups (overall P = 2.9 × 10-7). Our analysis highlights the impact of age on genetic susceptibility to ALL in Chinese patients.

Introduction Lupus erythematosus (LE) is an autoimmune disease with a strong influence of genetic and environmental factors. C-C motif chemokine receptor 5 (CCR5) gene expression may affect the development and intensity of LE. Aim To evaluate the possible association between the 32bp deletion in rs333 locus located within the CCR5 gene and the development of LE or the occurrence of various clinical symptoms in the course of the disease. Material and methods One hundred and twenty patients with LE (77 with systemic lupus erythematosus (SLE) and 43 with discoid lupus erythematosus (DLE)) and 100 healthy controls from the Polish population were genotyped for deletion in rs333. Results 32 bp deletion in the rs333 was significantly more frequent among healthy individuals than DLE patients. Moreover, heterozygotes and homozygotes with deletion in rs333 were significantly more frequent within the control group than the group of patients with discoid lupus erythematosus. In contrast, any statistically significant differences in allele or genotype frequencies between healthy persons and SLE patients were observed. Furthermore, nucleotide sequence variability of rs333 was not associated with certain clinical symptoms of LE patients. Conclusions Deletion in the rs333 might be a protective factor for DLE, but not SLE in the Polish population. Nevertheless further studies performed on larger populations are needed to confirm these observations.

Crop height (Ht), heading date (Hd), and grain yield (GY) are inter-related in wheat. Independent manipulation of each is important for adaptation and performance. Validated quantitative trait loci (QTLs) for all three co-locate on chromosome 3A in the Avalon×Cadenza population, with increased Ht, Hd, and GY contributed by Cadenza. We asked if these are linked or pleiotropic effects using recombinant lines, and showed that Ht and Hd effects are independent. The Chinese Spring equivalent to the newly defined Ht interval contained a gene cluster involved in cell wall growth and displaying high levels of differential transcript expression. The Hd locus is larger and rearranged compared with the reference genome, but FT2 (Flowering Locus T2) is of particular interest. The Hd effect acted independently of photoperiod and vernalization, but did exhibit seasonal genotype×environment interaction. Recombinants were phenotyped for GY in replicated field experiments. GY was most associated with Cadenza alleles for later Hd, supporting physiological studies using the same lines proposing that ‘late’ alleles at this locus increase spike fertility and grain number (GN). The work has uncoupled height from heading and yield, and shown that one of very few validated GY QTLs in wheat is probably mediated by phenological variation., There are only three validated wheat yield QTLs. Here, one of them was genetically dissected. This showed that the physiological basis of the yield effect is likely to be phenological.

Aeromonas are bacteria broadly spread in the environment, particularly in aquatic habitats and can induce human infections. Several virulence factors have been described associated with bacterial pathogenicity, such as the Type VI Secretion System (T6SS). This system translocates effector proteins into target cells through a bacteriophage-like contractile structure encoded by tss genes. Here, a total of 446 Aeromonas genome sequences were screened for T6SS and the proteins subjected to in silico analysis. The T6SS-encoding locus was detected in 243 genomes and its genes are encoded in a cluster containing 13 core and 5 accessory genes, in highly conserved synteny. The amino acid residues identity of T6SS proteins ranges from 78 to 98.8%. In most strains, a pair of tssD and tssI is located upstream the cluster (tssD-2, tssI-2) and another pair was detected distant from the cluster (tssD-1, tssI-1). Significant variability was seen in TssI (VgrG) C-terminal region, which was sorted in four groups based on its sequence length and protein domains. TssI containing ADP-ribosyltransferase domain are associated exclusively with TssI-1, while genes coding proteins carrying DUF4123 (a conserved domain of unknown function) were observed downstream tssI-1 or tssI-2 and escort of possible effector proteins. Genes coding proteins containing DUF1910 and DUF1911 domains were located only downstream tssI-2 and might represent a pair of toxin/immunity proteins. Nearly all strains display downstream tssI-3, that codes for a lysozyme family domain protein. These data reveal that Aeromonas T6SS cluster synteny is conserved and the low identity observed for some genes might be due to species heterogeneity or its niche/functionality. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-020-00405-y.

Cyclin-dependent kinase inhibitor 2A (CDKN2A) gene methylation has been paramount in the development of malignant masses. The purpose of the conducted research was to evaluate the mechanism and involvement of methylation in regards to the CDKN2A gene and the specific locus region in gastric cancer (GC) with comprehensive statistical analysis utilizing statistics acquired from The Cancer Genome Atlas (TCGA) database. Gene Set Enrichment Analysis (GSEA) revealed that the level of CDKN2A gene methylation and its locus in GC tissues was increased compared to para-cancerous tissues. In multivariate analysis, low methylation of CDKN2A gene, cg03079681, cg04026675, cg07562918, and cg13601799 locus were independently linked to better OS. In addition, the methylation of CDKN2A gene, cg00718440, cg03079681, cg04026675, cg07562918, cg10848754, cg14069088 and cg14430974 locus were negative correlated with CDKN2A gene expression. Meanwhile, the methylation of cg12840719 locus was positively correlated with CDKN2A gene expression. GSEA showed that hallmark_kras_signaling_dn, hallmark_myogenesis, and hallmark_epithelial_mesenchymal_transition pathways were enriched in the CDKN2A gene hypermethylation phenotype. Taken together, the low methylation of CDKN2A gene, cg03079681, cg04026675, cg07562918, and cg13601799 locus indicated a better prognosis in GC. The methylation levels of cg14069088 were most negatively correlated with CDKN2A gene expression. Hallmark_kras_signaling_dn, Hallmark_myogenesis, and hallmark_epithelial_mesenchymal_transition pathways might be important in the regulation of CDKN2A gene hypermethylation., Graphical abstract

A total of 251 Dura cross Pisifera (DxP) hybrid palms from six populations descending from six parental African Pisifera origins and involving 12 progenies were analyzed with 19 selected Simple Sequence Repeats (SSR) markers. A total of 110 alleles were produced, ranging from three to eight per SSR, with a mean of 5.8 alleles per SSR locus. Of these, 68.5% were considered shared alleles by more than one population and the remaining 31.5% were population specific alleles. They generated between six and 21 haplotypes in all populations, and depending on the SSR marker, between one and 10 haplotypes within populations. Various parameters for analyzing genetic variability, differentiation and genetic structure were computed using GenAlEx, Structure and Darwin software. The obtained results confirmed microsatellites as a robust, feasible and trustful method for obtaining DNA fingerprints, tracing the source of oil palm samples. With respect to the authenticity of materials or for solving legitimacy issues, accession belonging to each population by SSR markers could be distinguished, but additional SSR should be screened for improving this process.

Gene prioritisation at GWAS loci necessities careful assembly and examination of different types of molecular evidence to arrive at a set of plausible candidates. In many human traits, common small-effect mutations may subtly dysregulate the function of the very same genes which are impacted by rare, large-effect mutations causing Mendelian disease of similar phenotype. However, information on gene-Mendelian disease associations, rare pathogenic mutations driving the disease, and the disease phenotype ontology is dispersed across many data sources and does not integrate easily with enrichment analysis.MendelVar is a new webserver facilitating transfer of knowledge from Mendelian disease research into interpretation of genetic associations from GWAS of complex traits. MendelVar allows querying of pre-defined or LD-determined genomic intervals against a comprehensive integrated database to find overlap with genes linked to Mendelian disease. Next, MendelVar looks for enrichment of any Human Phenotype Ontology, Disease Ontology and other ontology/pathway terms associated with identified Mendelian genes. In addition, MendelVar provides a list of all overlapping pathogenic and likely pathogenic variants for Mendelian disease sourced from ClinVar.Inclusion of information obtained from MendelVar in post-GWAS gene annotation pipelines can strengthen the case for causal importance of some genes. Moreover, as genes with Mendelian disease evidence may make for more successful drug targets, this may be particularly useful in drug discovery pipelines. Taking GWAS summary statistics for male-pattern baldness, intelligence and atopic dermatitis, we demonstrate the use of MendelVar in prioritizing candidate genes at these loci which are linked to relevant enriched ontology terms. MendelVar is freely available athttps://mendelvar.mrcieu.ac.uk/

Primary membranous nephropathy, also known as idiopathic membranous nephropathy, is an autoimmune disease. As an autoimmune disease, genetic factors are essential in the pathogenesis of IMN. People pay more and more attention to genetics and bioinformatics. With the continuous improvement and development of high-throughput gene sequencing and genotyping technology, it has been confirmed that many genes and their single nucleotide polymorphisms are strongly correlated with IMN disease susceptibility. However, there are few studies on HLA-DQA1 and PLA2R gene polymorphisms and IMN susceptibility in China. The purpose of this study was to investigate whether PLA2R rs2715928 and rs16844715 are related to IMN, the correlation between five SNP loci of PLA2R and HLA-DQA1 and IMN, and the effect of gene-gene interaction among different genotypes of each locus on disease. In this study, 86 patients with IMN confirmed by renal biopsy in the first hospital of Harbin Medical University and 90 healthy controls were selected. All subjects were excluded from secondary membranous nephropathy, pregnant or breastfeeding women, severe primary disease of vital organs, severe infection, major surgery, and severe trauma. Seven selected SNP loci were genotyped using the IMLDR multiple SNP typing kit. Chi-square test and logistic regression were used to analyze the correlation between each SNP and IMN. The general clinical data and laboratory indicators of each subject were recorded, and the relationship between different genotypes and clinical manifestations was analyzed. Among the 7 SNP loci included in the study, except HLA-DQA1 rs2187668, the other 6 loci all met Hardy-Weiberg equilibrium test (P > 0.05). The allele distribution of PLA2R rs2715928 and rs16844715 was significantly different between the IMN group and the healthy control group, and it was closely related to IMN (P 0.05), and there was also statistical difference in the distribution of alleles of rs35771982, rs3749117, and rs4664308 between the IMN group and the healthy control group (P 0.05). PLA2R rs2715928 and rs16844715 are associated with susceptibility to IMN. The C allele of rs16844715, the A allele of rs2715928, the G allele of rs35771982, the T allele of rs3749117, and the A allele of rs4664308 are the dangerous genes of IMN. The combination of GG genotype at rs35771982 and AA genotype at rs2715928 poses the greatest risk of disease. Haplotype may affect susceptibility to IMN. The risk genotype had no effect on the clinical manifestations of IMN.